A computational approach for the analysis of epigenetic mechanisms in colorectal cancer
Presenter Type
UNO Graduate Student (Masters)
Major/Field of Study
Bioinformatics
Advisor Information
Dhundy Bastola
Location
MBSC304 - G (Masters)
Presentation Type
Oral Presentation
Start Date
24-3-2023 2:30 PM
End Date
24-3-2023 3:45 PM
Abstract
The availability of improved chromatin accessibility sequencing technologies such as ATAC-seq has increased our understanding of gene regulation mechanisms, especially in disease conditions such as cancer. In this study, we propose a computational tool that quantifies and links interactions between chromatin access, transcription factor binding, transcription factor mutations, and gene expression using publicly available colorectal cancer data. Our tool has been packaged using a workflow management system, enabling biologists and researchers to use this tool even if they lack the systems administration knowledge required for similar pipelines. Using this pipeline, we demonstrate that there is a link between chromatin accessibility and gene expression, especially in the context of transcription factor gene accessibility and SNP mutations. We also identified key transcription factor cascades upregulated in colon cancer patients, including the activation of the BCL-2 protein family via TP73 and apoptotic regulation via E2F1, MYC, and MYCN.
Scheduling
9:15-10:30 a.m., 10:45 a.m.-Noon, 1-2:15 p.m., 2:30 -3:45 p.m.
A computational approach for the analysis of epigenetic mechanisms in colorectal cancer
MBSC304 - G (Masters)
The availability of improved chromatin accessibility sequencing technologies such as ATAC-seq has increased our understanding of gene regulation mechanisms, especially in disease conditions such as cancer. In this study, we propose a computational tool that quantifies and links interactions between chromatin access, transcription factor binding, transcription factor mutations, and gene expression using publicly available colorectal cancer data. Our tool has been packaged using a workflow management system, enabling biologists and researchers to use this tool even if they lack the systems administration knowledge required for similar pipelines. Using this pipeline, we demonstrate that there is a link between chromatin accessibility and gene expression, especially in the context of transcription factor gene accessibility and SNP mutations. We also identified key transcription factor cascades upregulated in colon cancer patients, including the activation of the BCL-2 protein family via TP73 and apoptotic regulation via E2F1, MYC, and MYCN.